Exploring rate variation among and within sites in a densely sampled tree: species level phylogenetics of north american tiger beetles (genus cicindela)

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.     

Molecular evidence for broad-scale distributions in bdelloid rotifers: everything is not everywhere but most things are very widespread

The Baas-Becking's hypothesis, also known by the term 'everything is everywhere' (EisE), states that microscopic organisms such as bacteria and protists are globally distributed and do not show biogeographical patterns, due to their high dispersal potential. We tested the prediction of the EisE hypothesis on bdelloid rotifers, microscopic animals similar to protists in size and ecology that present one of the best cases among animals for the plausibility of global dispersal. Geographical range sizes and patterns of isolation by distance were estimated for global collections of the genera Adineta and Rotaria, using different taxonomic units: (i) traditional species based on morphology, (ii) the most inclusive monophyletic lineages from a cytochrome oxidase I phylogeny comprising just a single traditional species, and (iii) genetic clusters indicative of independently evolving lineages. Although there are cases of truly cosmopolitan distribution, even at the most finely resolved taxonomic level, most genetic clusters are distributed at continental or lower scales. Nevertheless, although 'everything is not everywhere', bdelloid rotifers do display broad distributions typical of those of other microscopic organisms. Broad dispersal and large population sizes might be factors lessening the evolutionary cost of long-term abstinence from sexual reproduction in this famous group of obligate parthenogens.     

The promising effects of BMP2 transfected mesenchymal stem cells on human osteosarcoma

Selective targeting of transfected mesenchymal stem cells (MSCs) carrying specific antioncogenes to the tumor was suggested as a treatment option. Bone morphogenetic protein-2 (BMP2) was shown to inhibit the proliferation and aggressiveness of osteosarcoma (OS) cells. Here, we aimed to assess the homing efficiency of intraperitoneally administered hMSCs transfected with BMP2 to the tumoral site and their effects on OS using an orthotopic xenograft murine model. Orthotopic xenograft murine model of OS in six-week-old female NOD/SCID mice using 143B cells was established. hMSCs transfected with BMP2 (BMP2⁺hMSC) were used. In vivo experiments performed on four groups of mice that received no treatment, or intraperitoneally administered BMP2, hMSCs, and BMP2⁺hMSCs. Histopathological and immunohistochemical studies were used to evaluate the pathological identification and to assess the dimensions and necrotic foci of the tumor, the features of lung metastases, and immunostaining against p27, Ki-67, and caspase-3 antibodies. The osteogenic differentiation markers BMP2, BMP4, COL1A1, OPN, OCN and PF4 evaluated using RT-PCR. The tumor dimensions in the hMSCs group were significantly higher than those of the remaining groups (p < 0.01). The number of metastatic foci in the BMP2⁺hMSCs group was significantly lower than those of the other groups (p < 0.01). The current results showed that the intraperitoneal route could be efficiently used for targeting hMSCs to the tumoral tissues for effective BMP2 delivery. In this study, the effects of BMP2 transfected hMSCs on human OS and metastasis were promising for achieving osteogenic differentiation and reduced metastatic process.     

Fungal Infections in COVID-19 Intensive Care Patients

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients’ hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.     

What can phylogenetics tell us about speciation in the Cape flora?

The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so-called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non-Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.     

The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

Nitrogen mineralisation and plant nitrogen acquisition in a nitrogen-limited calcareous grassland

A field study measured the rate of soil mineral N supply and its effects on plant biomass and N accumulation in a 13-year-old, naturally regenerating, calcareous grassland. Gross rates of N mineralisation (2 μg g⁻¹ day⁻¹, i.e. 0.69 kg ha⁻¹ day⁻¹), assessed using ¹⁵N pool dilution, were at the lower end of the range previously reported for grasslands. Weekly additions of liquid N fertiliser ([NH₄]₂SO₄, NH₄NO₃ or KNO₃) and, to a lesser extent the addition of water, increased plant growth substantially, demonstrating that the primary constraint to plant growth was low N availability. In plants that had received NO₃⁻, the activity of the inducible enzyme nitrate reductase in shoots initially increased in proportion to the amount of NO₃⁻ supplied. However, as above-ground herbage accumulated, nitrate reductase activity declined to similar low levels in all treatments, despite the continuance of the constant NO₃⁻ additions. The decline in NR specific activity reflected declining tissue NO₃⁻ concentrations, although total plant NRA may have remained constant during the period of study. The study has shown that plant growth is limited by low N mineralisation rates and indeed the soil is a sink for much added N. Low water availability provides an additional constraint on N mineralisation in this calcareous grassland soil. Any disturbances in the N cycle which increase the availability of mineral N will result in a substantial increase in plant growth within this ecosystem.     

Nitrogen uptake by crops,soil distribution and recovery of urea-N in a sorghum—wheat rotation in different soils under Mediterranean conditions

The N uptake by crops, soil distribution and recovery of 15N labelled urea-N (100 kg N ha-1) were investigated in a sorghum-wheat rotation in two silty clay soils (Foggia and Rieti Casabianca) and one silt loam soil (Rieti Piedifiume) under different mediterranean conditions. Non-exchangeable labelled NH4-N represented an important pool at both Rieti sites with higher values (p<0.05) under sorghum (14.0 and 24.6% of the urea N in the 0-20 cm layer at the end of the cropping season) than wheat whereas it was much less important in the Foggia soil (10.0% in the surface soil under sorghum). This is probably related to the clay minerals composition of the three soils; because vermiculite was present in both Rieti sites but not in the Foggia soil. At harvest from 4.4 to 5.3% of the urea N initially applied was present as microbial biomass N in the surface soil layer with no generally significant differences due to location and type of crops. Both sorghum and wheat N yields were higher in the driest site (Foggia) probably due to better light conditions, higher temperatures and irrigation during summer of the sorghum cropping period. The recovery of plant fertilizer N (about 21% for sorghum and 27% for wheat) and the percentage of N in the plant derived from the fertilizer (NDFF) were the lowest at Rieti-Casabianca probably as the result of the protection of immobilized fertilizer N against microbial mineralization by the swelling clays. The fertilizer N unaccounted for was nil or very low (10.8% at Rieti-Casabianca under wheat and 11.8 and 4.9% at Rieti-Piedifiume under sorghum and wheat, respectively). Urea-N losses occurred when Rieti Piedifiume and Rieti Casabianca soils were kept bare. In this case the urea N unaccounted for ranged from 12 to 56% of the urea N with higher losses in Rieti-Piedifiume than in Rieti-Casabianca. The higher recoveries in the latter soil were probably confirmed by the stabilizing effect of clays on the immobilized urea N. This revised version was published online in July 2006 with corrections to the Cover Date.     

Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree

Species-level phylogenies derived from DNA sequence data provide a tool for estimating diversification rates and how these rates change over time, but to date there have been few empirical studies, particularly on insect groups. We use a densely sampled phylogenetic tree based on mitochondrial DNA to investigate diversification rates in the North American tiger beetles (genus Cicindela). Using node ages estimated from sequence data and calibrated by biogeographical evidence, we estimate an average per-lineage diversification rate of at least 0.22 +/- 0.08 species/Myr over the time interval since the most recent colonization that led to a radiation within the continent. In addition, we find evidence for a weak, recent increase in the net diversification rate. This is more consistent with a late Pleistocene increase in the speciation rate than with a constant rate of background extinction, but the results are sensitive to the dating method and taxon sampling. We discuss practical limitations to phylogenetic studies of diversification rates.